Laser Based Identification of Molecular Characteristics

ABSTRACT

Enantiomers are characterized, identified, synthesized and/or modified with a shaped laser pulse. In another aspect of the present invention, binary shaping and circular polarization are employed with a laser pulse. A further aspect of the present invention provides a quarter-wave plate in combination with one or more pulse shapers.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with government support under National Science Foundation Contract No. CHE-0500661. The government may have certain rights in this invention.

BACKGROUND OF THE INVENTION

This invention generally relates to laser pulse shaping and more specifically to identifying molecular characteristics with a shaped laser pulse.

The almost exclusive handedness of the essential building blocks of life, illustrated by left-handed amino acids and right-handed carbohydrates, is one of the most intriguing scientific questions. Interest in the analysis of optically active compounds has grown considerably because of their importance in the biochemical and pharmaceutical industries. In a number of cases, one optically active form of a drug is effective while the other is inactive and can have undesirable side effects. The large-scale resolution of chiral compounds is presently carried out by crystallization, by chemical reaction with chiral reagents, by chromatography (particularly, simulated moving bed (SMB) techniques) or by newer technologies (for example, membranes/automated screening or counter current extractions). Drug discovery and metabolic analysis, however, involve very small quantities of optically active compounds and could benefit from much greater sensitivity. Similarly, the search for the origin of chiral purity found in living organisms requires the ability to identify extremely small quantities of chiral compounds that may be present in meteorites. Increased chiral sensitivity has already shown that right-handed amino acids are present in a number of organisms as post translational modifications.

Some studies have been conducted using polarization pulse shaping and an evolutionary learning algorithm selecting a limited number of tests from a very large quantity of shaping variable possibilities. One such experiment is discussed in T. Brixner, et al., “Quantum Control by Ultrafast Polarization Shaping,” Phys. Rev. Lett. 92, 20-8301 (2004).

SUMMARY OF THE INVENTION

In accordance with the present invention, enantiomers are characterized, identified, synthesized and/or modified by a shaped laser pulse. In another aspect of the present invention, binary shaping and circular polarization are employed with a laser pulse. A further aspect of the present invention provides a quarter-wave plate to convert horizontal and vertically polarized light into right or left circularly polarized light which allows for testing pure linear polarization by rotating the plate. In yet another aspect of the present invention, a laser system uses a first pulse shaper to introduce multiphoton intrapulse interference phase scan (hereinafter “MIIPS”) and linear chirp (if needed), a second pulse shaper to introduce binary and linear (for example, along the horizontal and vertical axes) polarization, and/or a quarter-wave plate to introduce circular polarization to the pulse. In yet another aspect of the present invention, a pulse shaper is used to introduce a combination of phase retardation and polarization rotation so as to prepare laser pulses having intense circularly polarized fields that rotate in the 10-100 fs timescale. Methods of using the present invention system are also provided.

Tailored laser pulses of the present invention are used for low concentration molecular identification, through chiral fields, which induce differential fragmentation of enantiomeric compounds. By coupling these intense laser pulses with a mass spectrometer, great (for example, single molecule) sensitivity and chiral resolution will be obtained. Enantiomeric pairs are non-superimposable mirror images of one another, often identified as right- or left-handed molecules with identical chemical properties, except when reacting with another chiral reagent such as enzymes. A mass spectrometer of the present invention uses chiral femtosecond laser pulses which act as photonic enzymes that preferentially fragment right or left handed molecules. Thus, the mass spectrometry of the present invention can now be used to identify all types of stereoisomers without additional chemical reactions, an important capability for a method with growing application to drug discovery and metabolic analysis. Conceptually, a chiral pulse causes asymmetric switching between right and left circularly polarized light, and leads to differential laser induced fragmentation and ionization in enantiomerically different molecules. A right-handed enantiomer will couple to the chiral electromagnetic field differently than a left handed enantiomer. Therefore, an intense pulse with a specific succession of right and left optical torques would thereby play the role of a chiral photonic enzyme, preferentially cleaving one of the enantiomers. Based on this physical model, the order of the applied set of torques should determine which of the enantiomer is preferentially cleaved. This is ideally suited for testing chirality in the manufacture of pharmaceuticals and protein sequencing, especially when the undesired chirality amino acids or molecules are in very low concentrations.

Furthermore, the present invention advantageously uses binary settings (0 and π, or right and left circular polarization, for example) instead of a continuum of overly large values to reduce the number of shaped pulses that need to be tested for effectiveness. This allows use of all possible shaped pulses but without the inaccuracies and delay of a genetic learning algorithm, with the preferred embodiment. Additional advantages and features of the present invention will become apparent from the following description taken in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a diagrammatic view of a preferred laser system of the present invention where a computer sends binary codes to a polarization shaper to flip the polarization of certain frequency regions of the pulse from x to y polarization. The shaped pulses then go through a quarter-wave plate and are focused on a mass spectrometer chamber where they cause preferential fragmentation of right- or left-handed molecules.

FIG. 2 is a graph showing a theoretical binary polarization pulse.

FIGS. 3 a and 3 b are graphs showing theoretical polarized propeller pulse shapes employed with the preferred embodiment laser system; two such cases (xy and yx) are shown and arrows indicate the prevalent rotation of the field.

FIG. 4 shows a first oscillator and shaper construction employed with the preferred embodiment laser system.

FIG. 5 shows a second oscillator, shaper and amplifier construction employed with the preferred embodiment laser system.

FIG. 6 shows a dual mask pulse shaper employed with the preferred embodiment laser system.

DETAILED DESCRIPTION

Referring to FIG. 1, a preferred embodiment of a laser system 11 of the present invention employs a femtosecond laser 13, operable of emitting laser beam pulses 15 of a duration of about 10-100 fs and preferably about 35 fs, a programmable computer controller 17 and a time-of-flight mass spectrometer 19. In the spectrometer, the electron impact source is replaced by amplified femtosecond laser pulses that are polarization shaped using a modified phase-amplitude pulse shaper 21. Pulse shaper 21 includes two gratings flanking a spatial light modulator which is at the Fourier plane. The laser pulse is dispersed in the frequency domain and discrete spectral regions are flipped from horizontal to vertical polarization. After spatial light modulator (“SLM”) 21, a quarter-wave length plate 23 is optionally used to convert the linear polarization, vertical and horizontal, into circular polarization, right and left, respectively. This device allows the controller to quickly test pure linear polarization by rotating the quarter-wave plate (either manually or with an automatically controlled electromagnetic actuator). The binary polarized pulses are then focused on a small concentration of molecular species in the gas phase (approximately 10⁴ molecules interact with each laser pulse). The resulting ions and fragment ions are detected and identified by their time-of-flight to the detector. The combination of polarization shaping and the quarter-wave plate results in fields with rapidly switching circularly polarized light as shown in FIGS. 2, 3 a and 3 b.

The laser, pulse shaper, controller, mass spectrometer and a multiphoton intrapulse interference phase scan (“MIIPS”) procedure are as disclosed in U.S. patent application Ser. No. 11/177,940, invented by Dantus et al. and filed on Jul. 8, 2005, which is incorporated by reference herein. Additionally, quarter-wave plate 23 is preferably a zero order, air spaced, CVI Laser, LLC Part No. QWPO-800-10-4-AS10 wave plate centered at the same wavelength as the fs laser pulse being used, preferably 800 nm. In the present example, a pulse shaper 21 is preferably a liquid crystal, dual mask, phase amplitude pulse shaper but other spatial light modulators based on acousto-optics or micro-electro-mechanical systems (“MEMS”) may alternately be used.

Pulse shaping as used herein preferably controls the phase and amplitude of different frequency regions within the bandwidth of a femtosecond laser beam pulse. This manipulation is usually done in the frequency domain and results in large frequency and temporal changes in the output field. Polarization shaping as used herein preferably controls the direction in which the electric field is pointing for different frequencies within the bandwidth of the femtosecond pulse. Polarization is beneficial since molecules usually align their dipole moments in the direction of the electric field. Fast changes in the electric field direction causes torques in the molecules.

More specifically, femtosecond oscillators come in three main categories: very compact fiber based systems (˜100-200 fs pulse duration), prism-compressed Ti:Sapphire systems (˜10-20 fs), and chirped mirror compressed Ti:Sapphire systems (<10 fs). The latter can produce pulses with duration of about 5 fs and a spectrum stretching from 600 nm up to 1100 nm, a 100 MHz repetition rate and energy per pulse up to 1 nJ. A schematic illustration of one laser system 31 used is presented in FIG. 4, and it incorporates a prism based pulse shaper with a spatial light modulator at the Fourier plane 33. For super-short pulses, a grating is preferred instead of a prism. Chirped mirrors 35 and optical wedges 37 compensate intracavity spectral phase distortions and allow generation of an octave spanning laser spectrum. The ultra-broad bandwidth shaper compensates phase distortions remaining from the oscillator and pre-compensates those farther down the beam path.

High energy laser systems can be divided broadly by their method of amplification into regenerative or multi-pass. Regenerative amplification provides a more efficient use of the gain and better stability; however, the regenerative amplification cavity results in greater phase distortions in the output pulse. Multi-pass amplification avoids some of these phase distortions by minimizing the number of optical elements and the number of times the laser pulse transmits through them. Shorter pulses can usually be achieved by multi-pass amplification but with greater alignment difficulty and lower pulse to pulse stability than the regenerative amplification systems. FIG. 5 shows a schematic of a high-energy laser system 51 capable of producing amplified phase shaped pulses with durations down to 30 fs, at a repetition rate of 1 kHz and with 0.7 mJ energy per pulse. With this system most of the distortions accumulated by the laser pulse inside the regenerative amplification cavity can be compensated by a pulse shaper 53. At the same time, the loss introduced by the shaper is compensated at an amplifier 55. The result is a very stable source that achieves 30 fs pulse duration (33 nm bandwidth). Pulse shaper 53 is introduced between an oscillator 57 and regenerative amplifier 55 to compensate nonlinear phase distortions introduced by the laser system itself and farther down the beam path, and to compensate for spectral narrowing in the amplifier.

Another dimension of laser control employed with the present invention, beyond phase and amplitude, is control of the polarization state of the field. Full control of polarization requires four independent degrees of freedom for each spectral component. When using two orthogonally oriented liquid crystal spatial light modulators 71, as illustrated in FIG. 6, the incident x-polarized light (E_(x)) exits with field components (E_(x), E_(y)) that depend on the phase retardance (φ_(A) and φ_(B)) introduced by the liquid crystal elements whose slow axis is oriented at 45° and −45°. This arrangement together with an output polarizer can be used to achieve phase and amplitude shaping at each pixel. It is also possible with this arrangement to generate a linearly polarized output along the x (“H”) or y (“V”) axes or circular left (“L”) or right (“R”) polarized light E′_(L)=(E_(x)−iE_(y))/2^(0.5); E′_(R)=(E_(x)+iE_(y))/2 ^(0.5). Using a 5-bit basis set π, H, V, L, R (see FIG. 6 and Table 1), phase amplitude and polarization effects are produced very efficiently. This set does not cover all possible arbitrary fields, but provides a digital binary approach for electric field manipulation that, in most cases, is sufficient to explore the sensitivity of the system to the different properties of the field. Thus, it is possible to introduce a π phase delay for each pixel and rotate polarization horizontally or vertically, or to create right or left circular polarization.

Table 1, phase retardance for A and B elements to achieve binary states “0”, φ_(A) ⁽⁰⁾, φ_(B) ⁽⁰⁾, and “1” φ_(A) ⁽¹⁾, φ_(B) ⁽¹⁾, in amplitude, phase, linear or circular polarization:

Amplitude^(a))(0, 1) Phase (0, π) Linear(H, V) Circular(L, R) “0” |E_(x)|² = 1 φ = 0 E_(x) = 1 E_(y) = 0 E_(L) = 1 E_(R) = 0 “1” |E_(x)|² = 0 φ = π E_(x) = 0 E_(y) = 1 E_(L) = 0 E_(R) = 1 φ_(A) ⁽⁰⁾, φ_(B) ⁽⁰⁾ 0 0 0 0 0 0 π/4 −π/4 φ_(A) ⁽¹⁾, φ_(B) ⁽¹⁾ π/2 −π/2 π/2 π/2 0 π −π/4 π/4 ^(a))An additional polarizer (x-oriented) is required at the output.

Rotation of the optical axis angle of the quarter-wave plate allows the operator to determine the ellipticity of polarization of the pulses. Circular polarizations are obtained at 45° and linear polarizations at 90°. Changing the optical axis angle provides a reliable control because it only affects the polarization of the beam but no other variable such as energy or dispersion. Occasionally, the femtosecond pulses are first linearly chirped in order to spread the different frequencies within the pulse in the time domain such that redder frequencies arrive first (positive chirp) or last (negative chirp).

The shaped and polarized femtosecond pulses of the present invention are preferably used to test for optically active or chiral characteristics of a specimen, more specifically for enantiomers and/or stereoisomers therein. In order to find the greatest enantiomeric specificity, the effect of 512 different circular-polarization shaped pulses are evaluated on the relative peak ratios of the different fragment ions of the samples. These pulses correspond to half of all possible 10-bit polarization functions that can be obtained by combining right- and left-circular polarization. From these 512 experiments, the pulses are found which give the greatest difference in ion product ratios (A/B) between the R- and S-enantiomers. From these pulses, mass spectra for both compounds are generated. The binary polarization that gives the greatest contrast between the compounds is automatically calculated and determined by controller 17. Using this polarization setting, a hundred measurements are made for each of the enantiomers.

In another theoretical example, this time with stretched laser pulses, it is expected that the pulses are a factor of two longer with the redder frequencies preceding the bluer ones or vice versa. Once again, one hundred measurements for each pulse type and molecule are employed; expected measured ratios between the fragments when circularly polarized negatively chirped pulses are used and then automatically evaluated by controller 17. The addition of negative or positive chirp may slightly increase the contrast ratio for the sample enantiomers. The contrast observed may be reversed when going from a negatively chirped pulse to one that is positively chirped. This reversal is predicted by the fact that the time order of the different frequency components of the pulse is reversed for positive or negative chirp.

By way of a theoretical example, a fragment ion corresponding to loss of a methyl group may exhibit the greatest sensitivity to the chiral laser pulses. Furthermore, the number of polarization flips introduced by the shaper correlates with the degree of contrast. This indicates that higher levels of discrimination will be possible using polarization phase functions with higher bit-resolution. Referring to FIGS. 3 a and 3 b, analysis of a number of electric fields that are found capable of enantiomeric resolution show a linear polarization component that precedes the large rotating component that is reminiscent to a propeller-like shape, in other words, with a helical and zig-zag radiating shape. The direction and curvature of the propeller component determines the enantio-selective photochemistry.

It is noteworthy that if the wave plate is rotated 45° then positive results are expected. But if it is rotated 0° or 90° then negative results are expected. Furthermore, pure left or right light is expected to generate negative results. All of the degrees are relative to the designed optical axis of the compound.

Two pulse shapers 33, 53 or 71 are provided so that the first one is controlled by the controller to correct phase distortions in the pulse and can impart both phase and amplitude shaping. The second shaper subsequently controls the final polarization of different frequency components in the shaped pulse. The pulse is preferably preceded by a long field of about 1-2 picoseconds that is plane polarized. This serves to align the molecular dipoles. Then, the shaped pulses should contain one or more propeller structures or characteristics to impart torques on the molecules. These torques break the molecules but enantiomers will twist in opposite directions. The propeller structures should have a duration between 20 fs and 1 ps to be effective on the molecular time scale. Such shaped pulses can be combined with a second linearly polarized laser that is also incident on the same molecules and aligns a second axis of the molecules. Accordingly, the molecules are aligned and oriented before the intense propeller pulse breaks the molecules. A final field is delayed in time and ionizes neutral fragments resulting from the interaction with the shaped pulses.

The present invention is used to test for chirality in the manufacture of pharmaceutical products. An electro-spray source is coupled to an ion trap mass spectrometer. Once the desired ions are trapped, the controller automatically interrogates them by the phase and polarization shaped pulses. This method advantageously interrogates ions such that the pulses only need to cleave one or more bonds but they do not have to ionize. This should increase enantiomer selectivity. Automated MIIPS pulse distortion detection and compensation in combination with polarization maximizes performance of the laser systems, especially for pharmaceutical manufacturing. Subsequent shaped pulses can then be automatically controlled by the controller to destroy undesired enantiomers in the product or compound.

Alternately, the present invention MIIPS shaping and polarization is employed in protein sequencing. This advantageously determines the handedness of the amino acids. The present invention should advantageously work even for very low concentrations in detecting and, optionally, destroying undesired amino acids with the incorrect chirality thereby removing poisons and diseases therein. In another variation, the present invention employs a circular dichroism spectrometer to determine a secondary protein structure of the specimen. The detected response of the specimen to differently shaped and/or polarized pulses provides information about the secondary structure of proteins and carbohydrates therein for analysis and/or determination by the controller.

It is noteworthy that the present invention's use of binary or 0/π settings of right and left polarization allows for testing of essentially all pulse shape values for enantiomer sensitivity testing, rather than prior experiments where only a limited quantity of shaping values were attempted since the genetic learning algorithms employed therein was overly time consuming. Thus, the system of the present invention preferably evaluates essentially all pulse shaping possibilities and then proceeds to carry out an exhaustive evaluation of the search space. The binary function reduces the search field in the present invention but without reducing effectiveness. This speeds up the analysis process considerably.

In summary, it is possible to prepare laser pulses capable of resolving enantiomeric pairs. At the fundamental level, the ability to prepare chiral pulses opens a window into the nature and dynamics of optical activity at the level of individual molecules. These observations can be developed for the reliable identification of a large number of enantiomeric species that would require analysis in areas such as metabolomics. A different application that could be envisioned would be the enantiomeric purification of a racemic mixture. Thus, enantiomeric identification and enhanced enantiomeric fragmentation of the present invention are ideally suited for testing chemical constituents for enantiomers for subsequent processing into pharmaceuticals. This type of laser pulse can also be used to determine the tertiary structure of proteins, for example beta-sheet or alpha-helix. It can also be used to identify enantiomeric characteristics in amino acid for use in protein sequencing. The pulse is automatically generated, shaped, chirped and polarized, then the pulse is used in a mass spectrometer, in combination with a controller, to automatically determine differences in fragmentation patterns, especially of enantiomers. Thereafter or simultaneously, the same pulse or a subsequent shaped and low intensity pulse can be used to either destroy undesired enantiomers (for example, left-handed molecules) in a mixed compound solution or to direct chemistry to prepare single-type enantiomers.

While various embodiments are disclosed, it is envisioned that further variations may fall within the scope of the present invention. For example, the pulse shaper may alternately provide 45° and/or circular polarization thereby negating the need for a separate quarter-wave plate. Furthermore, pulse durations of less than 1000 fs, less than 51 fs and possibly less than 10 fs may be used although some of the benefits of the present invention may not be realized. Similarly, the wavelength of the laser may be 800 nm, the fundamental wavelength of a titanium sapphire laser, its second harmonic may be at 400 nm or its third harmonic may be at 266 nm; such shorter second and/or third harmonic wavelengths may be advantageous for improved sensitivity in selective chemistry as compared to longer wavelengths which lead to field ionization and less sensitivity with molecular structures. For example, ultraviolet pulses of less than 100 fs may be used. Ultraviolet pulses having a center wavelength shorter than approximately 420 nm and a bandwidth greater than approximately 10 nm can be used with the present invention, especially with an actively controlled pulse shaper, and a pulse having a center wavelength less than 300 nm and a bandwidth greater than 5 nm is even more desirable. The present invention is also ideally suited for use in material processing, such as micromachining silicon microprocessor chips with a shaped and polarized laser pulse, especially employing MIIPS. While various materials and equipment types have been disclosed, it should be appreciated that a variety of other materials and hardware can be employed. It is intended by the following claims to cover these and any other departures from the disclosed embodiments which fall within the true spirit of this invention. 

1. A method of manufacturing a pharmaceutical compound, the method comprising: (a) emitting a laser beam; (b) shaping the laser beam; (c) polarizing the laser beam; (d) testing the pharmaceutical compound with the shaped and polarized laser beam; (e) automatically determining a chiral property of the pharmaceutical compound based on the test; and (f) creating a substantially helical and propeller-like direction and curvature of the polarized and shaped laser beam to cause enantiomeric selectivity.
 2. (canceled)
 3. The method of claim 1 further comprising emitting the laser beam with a pulse duration less than 100 femtoseconds.
 4. The method of claim 1 further comprising polarizing the laser beam with a quarter-waveplate after a shaper.
 5. The method of claim 1 further comprising electro-spraying the pharmaceutical compound.
 6. The method of claim 1 further comprising detecting a characteristic of the pharmaceutical compound with an ion trap mass spectrometer while interrogating ions in the pharmaceutical compound with phase and polarization shaped laser beam pulses.
 7. The method of claim 1 further comprising cleaving bonds in the pharmaceutical compound with phase and polarization shaped laser beam pulses.
 8. The method of claim 1 further comprising using multiphoton intrapulse phase scan to minimize distortions in the laser beam.
 9. The method of claim 1 further comprising using at least two of: (a) zero, (b) π, (c) right, and (d) left, circular polarization to test for effectiveness in determining chiral sensitivity to different laser beam shapes.
 10. The method of claim 1 further comprising: (a) correcting phase distortions of the laser beam with a first pulse shaper; and (b) polarizing the laser beam with a second pulse shaper after the correcting step.
 11. A method of manufacturing a pharmaceutical product, the method comprising: (a) emitting a set of laser beam pulses on the pharmaceutical product, each of the pulses having a duration of less than 100 femtoseconds; (b) shaping the pulses to control phase and amplitude in the pulses; (c) automatically detecting and compensating for distortions in the pulses, without a genetic learning algorithm; (d) polarizing the pulses after step (b) to control the electric field direction therein; and (e) detecting or changing a characteristic of the pharmaceutical product with the shaped and polarized pulses.
 12. The method of claim 11 further comprising creating a substantially helical and propeller-like direction and curvature of the polarized and shaped laser beam pulses to cause enantiomeric selectivity.
 13. The method of claim 11 further comprising polarizing the laser beam pulses with a quarter-wave plate after a shaper.
 14. The method of claim 11 further comprising electro-spraying the pharmaceutical product.
 15. The method of claim 11 further comprising detecting a characteristic of the pharmaceutical product with an ion trap mass spectrometer while interrogating ions in the pharmaceutical product with phase and polarization shaped laser beam pulses.
 16. The method of claim 11 further comprising cleaving bonds in the pharmaceutical product with phase and polarization shaped laser beam pulses.
 17. The method of claim 11 further comprising using multiphoton intrapulse phase scan to minimize distortions in the laser beam pulses.
 18. The method of claim 11 further comprising using at least two of: (a) zero, (b) π, (c) right, and (d) left, circular polarization to test for effectiveness in determining chiral sensitivity to different laser beam pulse shapes.
 19. A method of operating a laser system, the method comprising: (a) emitting a laser beam pulse; (b) minimizing phase distortions of the pulse by pulse shaping without a genetic learning algorithm; and (c) polarization shaping of the pulse after step (b).
 20. The method of claim 19 further comprising creating a substantially helical and propeller-like direction and curvature of the polarized and shaped laser beam to cause enantiomeric selectivity.
 21. The method of claim 19 further comprising: (a) emitting the pulse with a duration of less than 51 femtoseconds; and (b) minimizing phase distortions in an iterative manner using a series of laser beam pulses. 22-24. (canceled)
 25. The method of claim 19 further comprising detecting a characteristic of a pharmaceutical compound with an ion trap mass spectrometer while interrogating ions in the pharmaceutical compound with phase and polarization shaped laser beam pulses.
 26. The method of claim 19 further comprising cleaving bonds in a pharmaceutical compound with phase and polarization shaped laser beam pulses.
 27. The method of claim 19 further comprising automatically destroying undesired enantiomers with the pulse.
 28. A method of operating a laser system, the method comprising using at least two of: (a) vertical linear, (b) horizontal linear, (c) right circular, and (d) left circular, pulse shapes to test essentially all possible pulse shapes for determining chiral sensitivity in a specimen. 29-31. (canceled)
 32. The method of claim 28 further comprising electro-spraying the specimen which is a pharmaceutical compound.
 33. The method of claim 28 further comprising cleaving bonds in the specimen which is a pharmaceutical compound with phase and polarization shaped laser beam pulses.
 34. The method of claim 28 further comprising using multiphoton intrapulse phase scan to minimize distortions in the laser beam pulse.
 35. The method of claim 28 further comprising: (a) correcting phase distortions of the laser beam pulse with a first pulse shaper; and (b) polarizing the laser beam pulse with a second pulse shaper after the correcting step.
 36. The method of claim 28 further comprising using all four of the pulse shapes.
 37. A method of operating a laser system, the method comprising: (a) emitting a laser pulse; (b) shaping the pulse including polarization; and (c) detecting secondary structure of a specimen in response to interaction of the shaped pulse on the specimen.
 38. The method of claim 37 wherein the secondary structure includes a secondary protein structure.
 39. The method of claim 37 wherein the secondary structure includes a secondary carbohydrate structure. 40-50. (canceled)
 51. A laser system comprising: a laser operably emitting laser beam pulses, each being less than 1000 fs in duration and having a bandwidth greater than 10 nm; at least one device operably linearly and circularly polarizing the pulses; a spectrometer; and a controller connected to the spectrometer and device; the controller automatically causing the device to vary the polarization based at least in part on a signal from the spectrometer, and without a genetic learning algorithm. 52-57. (canceled)
 58. A laser system comprising: an ultraviolet laser pulse having a center wavelength shorter than about 420 nm and a bandwidth greater than about 10 nm; an adaptive shaper operably varying a characteristic of the pulse; and a detector operably detecting a chiral property of a specimen.
 59. The laser system of claim 58 further comprising the detector operably detecting a characteristic of the pulse and a controller automatically varying the performance of the shaper based on a signal from the detector. 60-62. (canceled)
 63. A laser system comprising: laser pulses having a second or third order harmonic wavelength; a shaper operably varying a characteristic of the pulses; a polarizer operably polarizing the pulses; and a detector operably detecting a chiral characteristic of a specimen acted upon by the shaped and polarized pulses. 64-67. (canceled)
 68. A method of manufacturing a pharmaceutical compound, the method comprising: (a) emitting a laser beam; (b) shaping the beam; (c) polarizing the laser beam; (d) using at least two of: (i) zero, (ii) π, (iii) right, and (iv) left, circular polarization to test for effectiveness in determining chiral sensitivity to different laser beam shapes; and (e) detecting or changing a characteristic of the pharmaceutical compound with the shaped and polarized beam.
 69. The method of claim 68 further comprising only using binary settings of right and left polarization for testing beam shape values for enantiomer sensitivity.
 70. The method of claim 68 further comprising automatically detecting and compensating for distortions in the beam without a genetic learning algorithm.
 71. The method of claim 68 further comprising protein sequencing with the shaped and polarized beam. 